Hi,
On Tue, Apr 17, 2012 at 10:22 AM, Alfredo Quevedo
<alfredoq.fcq.unc.edu.ar> wrote:
> Dan, as you state I assumed that "closeswaters" and "closest" are the
> same. However I get different results with the same script:
OK, I understand now - and yes you're right, the behavior is different
- the ptraj version of the command strips only waters, while the
cpptraj command strips everything not in the mask. This was an
oversight on my part when I originally ported the command. A patch
will be released soon for cpptraj that will make the behavior
consistent with ptraj. Thanks again for the report.
-Dan
>
> 1) ptraj input:
>
> ***********************************************************
>
> trajin complex.mdcrd 1 10
> center :1-554
> image center familiar
> strip :Na+
> closestwaters 10 :LIG
> trajout complex_closestWAT.mdcrd trajectory
>
> ***********************************************************
>
> with this output I get the trajectory containing the whole complex with
> 10 molecules sorrounding the ligand.
>
>
> 2) cpptraj input
>
>
> ******************************************************
>
> complex.mdcrd 1 10
> center :1-554
> image center familiar
> strip :Na+
> closest 10 :LIG first closestout fila.dat outprefix closest
> trajout complex_closestWAT.mdcrd trajectory
>
> ******************************************************
>
> In this case I get a trajectory containing only the ligand sorrounded by
> 10 water molecules.
>
>
> best regards
>
> Alfredo
>
>
>>
>> Hi,
>>
>> On Tue, Apr 17, 2012 at 8:44 AM, Alfredo Quevedo
>> <alfredoq.fcq.unc.edu.ar> wrote:
>>> The point is that the calculation of distances is
>>> rather slow, that is why I wanted to run it in parallel using cpptraj.
>>> Unfortunately I find that the "closestwater" command is not included in
>>> cpptraj.
>>
>> I'm confused by this. The 'closest' command is the same as the
>> 'closestwater' command. In ptraj 'closestwater' was just the longer
>> name for the shorter alias 'closest'. So in that sense 'closestwater'
>> is in cpptraj, just now it is called 'closest'. In addition, this
>> command is one of the actions in cpptraj that is OpenMP parallelized;
>> let me know if you have problems compiling with OpenMP or getting the
>> OpenMP version of cpptraj to work correctly.
>>
>> -Dan
>>
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>
> --
> ************************************************************************
> Dr. Mario Alfredo Quevedo.-
> Departamento de Farmacia.-
> Facultad de Ciencias Químicas.-
> Universidad Nacional Córdoba.-
> 5000 Córdoba, Argentina
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Received on Tue Apr 17 2012 - 08:00:04 PDT
